geney 1.3.71__py2.py3-none-any.whl → 1.3.73__py2.py3-none-any.whl

geney/splicing_utils.py

@@ -540,7 +540,12 @@ def process_pairwise_epistasis_explicit(mid, engine='spliceai'):
     lower_pos, upper_pos = int(parts[2]), int(parts[6])
 
     # Load gene and its transcript (as pre-mRNA)
-    g = Gene.from_file(parts[0]).transcript().generate_pre_mrna()
+    g = Gene.from_file(parts[0]).transcript()
+
+    if g is not None:
+        g.generate_pre_mrna()
+    else:
+        return pd.DataFrame()
 
     # If gene is on the reverse strand, swap positions and set factor to -1.
     if g.rev:
@@ -597,8 +602,18 @@ def process_pairwise_epistasis_explicit(mid, engine='spliceai'):
     ).round(2)
 
     # Drop columns that do not vary (only one unique value).
-    acceptors_df = acceptors_df.loc[:, acceptors_df.nunique() > 1]
-    donors_df = donors_df.loc[:, donors_df.nunique() > 1]
+    # acceptors_df = acceptors_df.loc[:, acceptors_df.nunique() > 1]
+    # donors_df = donors_df.loc[:, donors_df.nunique() > 1]
+    if (acceptors_df.nunique() > 1).any():
+        acceptors_df = acceptors_df.loc[:, acceptors_df.nunique() > 1]
+    else:
+        acceptors_df = acceptors_df.iloc[:, [0]]
+
+    # For donors_df:
+    if (donors_df.nunique() > 1).any():
+        donors_df = donors_df.loc[:, donors_df.nunique() > 1]
+    else:
+        donors_df = donors_df.iloc[:, [0]]
 
     # Further filter acceptors: keep only columns where the value in the second row is < 0.1.
     # (Assumes that the second row (iloc[1]) represents a specific measure you wish to threshold.)
@@ -607,13 +622,7 @@ def process_pairwise_epistasis_explicit(mid, engine='spliceai'):
     def add_features_and_filter(df):
         if df.shape[1] == 0:
             return df  # Nothing to process if no columns remain.
-        # Compute the residual:
-        #   (row 3 - row 0) minus ( (row 1 - row 0) + (row 2 - row 0) )
         df.loc['residual'] = (df.iloc[3] - df.iloc[0]) - ((df.iloc[1] - df.iloc[0]) + (df.iloc[2] - df.iloc[0]))
-        # Keep only columns where the absolute residual exceeds 0.1.
-        # df = df.loc[:, df.loc['residual'].abs() > 0.1]
-        # if df.shape[1] == 0:
-        #     return df
         # Compute deviations relative to the baseline (row 0)
         df.loc['deviation1'] = df.iloc[1] - df.iloc[0]
         df.loc['deviation2'] = df.iloc[2] - df.iloc[0]
@@ -631,31 +640,7 @@ def process_pairwise_epistasis_explicit(mid, engine='spliceai'):
         acceptors_df.loc['site_type', :] = 1
 
     df = pd.concat([acceptors_df, donors_df], axis=1)
-    #
-    # if df.shape[1] == 0:
-    #     return df
-    #
-    # mask = df.apply(
-    #     lambda col: (
-    #             (abs(col['residual']) > 0.1) and
-    #             (abs(col['deviation1'] + col['deviation2']) < 0.1)
-    #     ),
-    #     axis=0
-    # )
-    #
-    # df.loc['synergistic'] = 0
-    # df.loc['synergistic', mask] = 1
-    #
-    # mask = df.apply(
-    #     lambda col: (
-    #             (abs(col['residual']) > 0.1) and
-    #             (abs(col['total_deviation']) <= 0.25)
-    #     ),
-    #     axis=0
-    # )
-    #
-    # df.loc['antagonistic'] = 0
-    # df.loc['antagonistic', mask] = 1
+
     df.loc['mut_id'] = mid
     df.loc['engine'] = engine
     df.loc['site'] = df.columns

{geney-1.3.71.dist-info → geney-1.3.73.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geney
-Version: 1.3.71
+Version: 1.3.73
 Summary: A Python package for gene expression modeling.
 Home-page: https://github.com/nicolaslynn/geney
 Author: Nicolas Lynn

{geney-1.3.71.dist-info → geney-1.3.73.dist-info}/RECORD

@@ -16,7 +16,7 @@ geney/pangolin_utils.py,sha256=9jdBXlOcRaUdfi-UpUxHA0AkTMZkUF-Lt7HVZ1nEm3s,2973
 geney/power_utils.py,sha256=MehZFUdkJ2EFUot709yPEDxSkXmH5XevMebX2HD768A,7330
 geney/seqmat_utils.py,sha256=wzb3PX5it5bpIFQvcxyzlxfhoJTbHHbsjg0rzh05iVs,19753
 geney/spliceai_utils.py,sha256=tVY0T6F6l3fNoaktpn7Kq0oH5ZM0ThFYt9nPi_lfakw,3077
-geney/splicing_utils.py,sha256=-4Xd7durnm3362IYn_7RO7dOZkPRadWZcRZgvTF2Thg,47786
+geney/splicing_utils.py,sha256=mAiZXBzb0IzZ_O0CIhxR36q8H9xqPXJOUk2fU1UTqc8,47313
 geney/survival_utils.py,sha256=KnAzEviMuXh6SnVXId9PgsFLSbgkduTvYoIthxN7FPA,6886
 geney/tcga_utils.py,sha256=D_BNHm-D_K408dlcJm3hzH2c6QNFjQsKvUcOPiQRk7g,17612
 geney/tis_utils.py,sha256=la0CZroaKe5RgAyFd4Bf_DqQncklWgAY2823xVst98o,7813
@@ -25,7 +25,7 @@ geney/translation_initiation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NM
 geney/translation_initiation/tis_utils.py,sha256=AF3siFjuQH-Rs44EV-80zHdbxRMvN4woLFSHroWIETc,4448
 geney/translation_initiation/resources/kozak_pssm.json,sha256=pcd0Olziutq-6H3mFWDCD9cujQ_AlZO-iiOvBl82hqE,1165
 geney/translation_initiation/resources/tis_regressor_model.joblib,sha256=IXb4DUDhJ5rBDKcqMk9zE3ECTZZcdj7Jixz3KpoZ7OA,2592025
-geney-1.3.71.dist-info/METADATA,sha256=qwuLQNso5Kv8Xs23-90MykN695SOLmAkMbpaco1FbhM,990
-geney-1.3.71.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
-geney-1.3.71.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
-geney-1.3.71.dist-info/RECORD,,
+geney-1.3.73.dist-info/METADATA,sha256=zBDPXEkIQIf58meB91wGEvGGPfe1rlR7-XZX9toMKdM,990
+geney-1.3.73.dist-info/WHEEL,sha256=AHX6tWk3qWuce7vKLrj7lnulVHEdWoltgauo8bgCXgU,109
+geney-1.3.73.dist-info/top_level.txt,sha256=O-FuNUMb5fn9dhZ-dYCgF0aZtfi1EslMstnzhc5IIVo,6
+geney-1.3.73.dist-info/RECORD,,